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After much research on Harmony, Flirc, and Shield forums, I finally have a setup for my Harmony remote that records all Shield functions correctly to the Flirc. My biggest issue was trying to find a workaround so I didn't have to use CEC with the Shield. My setup includes a Harmony activity for the Shield and all the Harmony button mapping. It also includes a feature to wake up the Shield and power off the Shield when switching activities or powering off all devices. My setup works for the Harmony 600 and 700 series remotes, so some modifications my be necessary for other Harmony remotes. See the attachment for details. Make sure to read through the entire document before starting your programming and it will make more sense to you. It looks somewhat daunting, but if you are already familiar with programming a Flirc device and Harmony remote, it's only about 30 minutes of programming time.
Harmony, Shield, & FLIRC Programming.pdf
Edit: Added the FLIRC config file
FLIRC-Shield-Harmony Config.fcfg